ArticleNucleic acids research2015
Estimating binding properties of transcription factors from genome-wide binding profiles.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 37 citations in OpenAlex.
- The Algorithm for Reversible Jump Inference of Motifs.bioRxiv : the preprint server for biology · 2025Article
- Identification of mammalian transcription factors that bind to inaccessible chromatin.Nucleic acids research · 2023Article
- The role of insulators and transcription in 3D chromatin organization of flies.Genome research · 2022Article
- Deep learning for MYC binding site recognition.Frontiers in bioinformatics · 2022Article
- Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework.Computational and structural biotechnology journal · 2020Article
- An in silico analysis of robust but fragile gene regulation links enhancer length to robustness.PLoS computational biology · 2019Article
- COMPASS for rapid combinatorial optimization of biochemical pathways based on artificial transcription factors.Nature communications · 2019Article
- Chromatin architecture reorganization during neuronal cell differentiation inGenome research · 2019Article
- RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding.Computational and structural biotechnology journal · 2019Article
- Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors.Genome biology · 2018Article
- Transcription factor target site search and gene regulation in a background of unspecific binding sites.Journal of theoretical biology · 2018Article
- A novel method for improved accuracy of transcription factor binding site prediction.Nucleic acids research · 2018Article
- Transcription factor binding site clusters identify target genes with similar tissue-wide expression and buffer against mutations.F1000Research · 2018Article
- Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding.Nucleic acids research · 2017Article
- Designing and interpreting 'multi-omic' experiments that may change our understanding of biology.Current opinion in systems biology · 2017Review
- NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data.BMC genomics · 2017Article
- HspB5 correlates with poor prognosis in colorectal cancer and prompts epithelial-mesenchymal transition through ERK signaling.PloS one · 2017Article
- Article
- Reliable scaling of position weight matrices for binding strength comparisons between transcription factors.BMC bioinformatics · 2015Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The binding of transcription factors (TFs) is essential for gene expression. One important characteristic is the actual occupancy of a putative binding site in the genome. In this study, we propose an analytical model to predict genomic occupancy that incorporates the preferred target sequence of a TF in the form of a position weight matrix (PWM), DNA accessibility data (in the case of eukaryotes), the number of TF molecules expected to be bound specifically to the DNA and a parameter that modulates the specificity of the TF. Given actual occupancy data in the form of ChIP-seq profiles, we backwards inferred copy number and specificity for five Drosophila TFs during early embryonic development: Bicoid, Caudal, Giant, Hunchback and Kruppel. Our results suggest that these TFs display thousands of molecules that are specifically bound to the DNA and that whilst Bicoid and Caudal display a higher specificity, the other three TFs (Giant, Hunchback and Kruppel) display lower specificity in their binding (despite having PWMs with higher information content). This study gives further weight to earlier investigations into TF copy numbers that suggest a significant proportion of molecules are not bound specifically to the DNA.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.